LAMMPS (8 Jul 2015)
units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3

read_data data.swm4-ndp
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2500 atoms
  scanning bonds ...
  1 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  2000 bonds
  reading angles ...
  500 angles
  4 = max # of 1-2 neighbors
  3 = max # of 1-3 neighbors
  3 = max # of 1-4 neighbors
  4 = max # of special neighbors

pair_coeff    1    1      0.210939     3.183950  # ODw ODw
pair_coeff    *   2*      0.000000     0.0

group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES

variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0

neighbor 2.0 bin

timestep 1.0

fix DRUDE all drude C N N D

velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345

delete_bonds ATOMS multi
PPPM initialization ...
  G vector (1/distance) = 0.217457
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.197288
  estimated relative force accuracy = 0.000594128
  using double precision FFTs
  3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 14
  2000 total bonds, 500 turned on, 1500 turned off
  500 total angles, 0 turned on, 500 turned off
  0 total dihedrals, 0 turned on, 0 turned off
  0 total impropers, 0 turned on, 0 turned off

comm_modify vel yes
compute TATOM ATOMS temp/com
compute TEMP all temp/drude

fix DTDIR all drude/transform/direct
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
500 rigid bodies with 2000 atoms
  0.832099 = max distance from body owner to body atom
fix_modify RIGID temp TATOM press thermo_press
WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395)
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
fix NVT DRUDES nvt temp 1 1 100.0
fix DTINV all drude/transform/inverse

thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20

run 2000
PPPM initialization ...
  G vector (1/distance) = 0.217457
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.197288
  estimated relative force accuracy = 0.000594128
  using double precision FFTs
  3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Memory usage per processor = 24.8361 Mbytes
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] 
       0            0    4568.0415    903.41148      3664.63    623.46454            0    2890.2449    157955.66   -157804.74    244591.08        13824    202.18534    295.64644    14.858785 
      20    1.5779378    3742.6839    5338.7884   -1596.1045    567.30749            0    662.23765    155098.36   -157924.01    31679.424    13979.574    1194.8318    1690.2246    201.65659 
      40    3.2595179    2752.8331    4407.7651    -1654.932    793.00135            0    870.33079    154593.76   -157912.03    27394.571     14278.56    986.46688    1450.7477    55.932382 
      60    4.9160559     1995.591    3982.0372   -1986.4462    660.67737            0    750.60932    154536.67    -157934.4    22230.527    14691.401     891.1881    1315.7324    40.317107 
      80    6.5368109    1376.4607    3451.5429   -2075.0822    617.73899            0     606.3673    154625.69   -157924.88     17342.36    15201.343    772.46238    1147.1933    21.455584 
     100    8.1206679    885.61474    3037.6308   -2152.0161    536.23281            0    448.92334    154793.04   -157930.22     13263.15    15783.251    679.82802    1011.6854      14.7536 
     120    9.6622779    487.58833    2926.9844    -2439.396    534.45257            0    332.92672    154624.58   -157931.35    8680.1072    16409.225    655.06511     977.0118    9.8615914 
     140    11.151044    159.92993    2531.0941   -2371.1641    507.26614            0    248.61605     154802.7   -157929.75    6399.7614    17052.819    566.46405    845.55948    7.1402545 
     160    12.594065   -100.92554    2408.1685   -2509.0941    490.99513            0    134.36067    154800.59   -157935.04    3836.8939     17698.15    538.95306    805.19219    5.3968881 
     180     13.99897   -313.40437    2221.7416   -2535.1459    469.97779            0    75.805558    154853.24   -157934.17    1959.0151    18334.826    497.23032    743.14066    4.4151864 
     200    15.366489   -490.94535    2067.2605   -2558.2059    455.16264            0    77.545085    154841.14   -157932.06    1193.2843    18956.449    462.65715     691.7234    3.5993432 
     220    16.600555   -642.90899    1962.7268   -2605.6358      481.409            0     64.82886    154779.27   -157931.14    257.97318    19559.017    439.26229    657.06726    2.7738353 
     240    17.905356   -770.44499     1795.759    -2566.204    467.25833            0     68.82314    154829.98   -157932.26    19.366424    20139.417    401.89456    601.24562    2.3886434 
     260    19.179106   -878.63388    1752.9497   -2631.5836    476.38325            0    71.933328    154747.16   -157927.06   -779.27927    20696.165    392.31375    587.06527    2.0260796 
     280    20.338816   -971.86313    1649.5511   -2621.4143    473.83718            0    58.460942     154779.6   -157933.32   -1008.6839     21226.44    369.17293     552.5314    1.7176302 
     300    21.569212   -1057.5245    1580.9766   -2638.5012    480.33124            0    92.042617    154721.84   -157932.72   -1273.0871    21728.981    353.82581    529.63244    1.5049172 
     320    22.749114   -1132.8131    1507.0527   -2639.8658    477.51281            0    107.39942    154707.48   -157932.26   -1098.1682    22203.702    337.28149    504.90539    1.3591193 
     340    23.866651   -1199.4814    1495.1233   -2694.6047    479.99745            0    106.51864    154656.08    -157937.2   -1429.2857    22652.428    334.61166    500.95977    1.2462004 
     360    25.082959   -1264.8469    1440.8985   -2705.7454    491.71868            0    107.29672     154624.8   -157929.57   -1584.3973    23073.056    322.47604    482.79111    1.2009575 
     380    26.115491   -1323.6479     1376.047    -2699.695     497.4857            0    130.64748    154603.75   -157931.58   -1822.0261    23465.375    307.96215    461.10877    1.0530068 
     400    27.098619   -1373.3921     1374.977   -2748.3691    504.29487            0    124.46131    154555.55   -157932.67   -2021.5919    23828.229    307.72267    460.78429   0.98399317 
     420    28.070089   -1426.0355    1375.3813   -2801.4168      515.478            0    142.00079    154473.71   -157932.61   -2208.8244     24160.02    307.81316    460.97813   0.86759754 
     440    29.088747   -1476.2448    1329.2669   -2805.5117    535.72651            0     196.6858     154393.5   -157931.42   -1618.3009    24460.675    297.49266    445.47247   0.93805929 
     460    30.039555   -1527.7744    1320.4118   -2848.1861    568.66085            0    263.35802    154252.43   -157932.64   -1494.5444    24734.828    295.51087    442.54962   0.84234766 
     480     30.98472   -1576.2009    1300.9323   -2877.1332    594.86236            0    314.31593    154144.87   -157931.19   -1089.6762    24985.934    291.15132    436.02273   0.82622001 
     500    31.921181   -1626.4788    1317.6697   -2944.1486    623.62396            0    334.61944    154026.32   -157928.71   -1168.0859    25218.234    294.89719    441.63818   0.82542904 
     520    32.850868    -1678.487    1262.6568   -2941.1438    633.47682            0    363.44379    153992.91   -157930.98   -1163.3304    25431.978    282.58518    423.21273   0.76490406 
     540    33.831238   -1726.1374    1271.5003   -2997.6376    640.74261            0    345.52688    153948.98   -157932.89   -1537.3705    25626.826    284.56437    426.19842   0.72713952 
     560    34.751061   -1771.2597     1269.233   -3040.4927    644.30805            0     317.8435    153929.28   -157931.92   -1722.5181    25799.253    284.05695    425.41542   0.77189915 
     580    35.665466   -1815.0265     1246.413   -3061.4395    683.24088            0    371.72686    153815.69    -157932.1   -1494.5382    25947.498    278.94979    417.73291   0.82565978 
     600    36.573731   -1858.3541    1196.3137   -3054.6678    696.06741            0    437.52527    153744.09   -157932.35   -954.95797    26075.526    267.73745    400.95599   0.76490653 
     620    37.479106   -1899.6548    1179.8195   -3079.4743    696.68256            0    400.17078    153755.86   -157932.18    -1545.546    26187.542    264.04602    395.42296   0.76404516 
     640    38.439799   -1936.5953    1175.0129   -3111.6082    690.67817            0    392.53009    153736.67   -157931.49   -1651.1722    26278.598    262.97029    393.82361   0.73771389 
     660    39.342719   -1974.4946     1176.582   -3151.0766    687.10898            0    368.78109    153725.56   -157932.53   -1642.1352    26346.954    263.32147    394.35652   0.72471807 
     680    40.233007   -2011.9427    1170.7634   -3182.7062     704.7553            0    376.83243    153670.03   -157934.32   -1891.1355    26391.697    262.01926    392.39338   0.74699214 
     700    41.124436   -2051.0351    1135.0688   -3186.1039    725.49013            0    408.02789    153612.64   -157932.26    -1554.558    26411.443    254.03072    380.39243   0.79925352 
     720    42.014817   -2087.2728    1127.2712    -3214.544    747.73788            0    483.80639    153486.98   -157933.07   -1246.9189    26409.313    252.28561    377.77086   0.81053421 
     740    42.908141   -2122.8783    1145.0602   -3267.9385    791.69089            0    545.96341    153327.46   -157933.05   -1064.8488    26390.224    256.26683    383.71741   0.85313379 
     760    43.799068   -2155.8658    1189.0654   -3344.9312    789.63603            0    492.27945    153309.89   -157936.74   -1502.4138     26356.52    266.11528     398.4847   0.84422302 
     780    44.690825   -2197.1759    1166.0016   -3363.1774    813.89866            0    521.14986    153239.56   -157937.79   -1316.1431    26304.488    260.95354    390.75511   0.82849551 
     800     45.65434   -2236.6034    1147.1342   -3383.7376    858.77647            0    581.50775    153111.46   -157935.49   -1059.9568    26235.547    256.73099     384.3699   0.93971538 
     820    46.655089   -2273.5686    1128.3309   -3401.8996    876.66305            0     635.8842    153020.42   -157934.87   -522.03009     26154.47    252.52277    378.09253   0.87820184 
     840    47.581215   -2310.5392    1107.1453   -3417.6845       906.73            0    663.59923    152946.29   -157934.31   -660.73299    26066.561    247.78139    370.96848    0.9116362 
     860    48.461532   -2342.7319    1130.0857   -3472.8176    942.10066            0     680.8635    152839.09   -157934.87   -541.95751    25971.767    252.91551    378.61448    1.0117334 
     880    49.348792   -2377.0856    1100.1359   -3477.2215    941.37588            0    700.77054    152814.73    -157934.1   -443.18233    25871.504    246.21267    368.56741    1.0107473 
     900    50.240716   -2408.6694    1120.4615    -3529.131    953.77939            0    683.49952    152768.93   -157935.34   -805.27426    25765.603    250.76159    375.35036    1.0825367 
     920    51.130132   -2442.8312    1111.7289     -3554.56    950.77289            0    674.01395     152754.6   -157933.95   -905.29746    25651.192    248.80721    372.46424    0.9955159 
     940     52.02236   -2475.7651    1083.1001   -3558.8652    929.08218            0    652.94438    152792.16   -157933.05   -788.57962    25527.175    242.40003     362.8243    1.0666862 
     960    52.924057   -2508.9913    1065.8755   -3574.8668    958.92048            0    698.81111    152699.64   -157932.24   -628.47136    25394.225    238.54512    356.97396    1.2103698 
     980    53.828788   -2536.4577    1080.5323     -3616.99    965.47688            0    709.51639    152642.64   -157934.62   -711.96055    25254.689    241.82535    361.89287    1.2066617 
    1000    54.736123   -2567.3495    1049.6524   -3617.0019    961.00327            0    711.26219    152645.74   -157935.01   -767.44539    25108.887    234.91437    351.52221    1.2288643 
    1020    55.707224   -2595.1206    1073.4918   -3668.6124    974.79134            0    682.20149    152609.52   -157935.12   -1086.5823    24955.503    240.24966    359.53972    1.1890491 
    1040    56.677394   -2626.5258    1072.5969   -3699.1227    1013.3934            0    711.73335    152511.92   -157936.17   -993.59976    24792.452    240.04939    359.23966    1.1887504 
    1060    57.582305   -2655.4118    1059.0687   -3714.4806    1011.7018            0    747.43846    152460.24   -157933.86   -555.51961    24621.133    237.02176     354.6316    1.3280226 
    1080    58.451085   -2684.3286    1093.9034    -3778.232    1041.5624            0    765.98574    152348.29   -157934.07   -993.29607    24444.559    244.81782    366.39031     1.183205 
    1100    59.320593   -2716.1558    1073.5935   -3789.7493    1046.6309            0     741.4524    152358.32   -157936.15   -1031.9439    24260.537    240.27243      359.559    1.2187426 
    1120    60.197434   -2748.4358    1043.9493   -3792.3851    1050.7685            0    732.61894    152361.65   -157937.42   -1173.2273    24068.431      233.638    349.62448    1.1977845 
    1140    61.088693   -2777.1545    1036.6106   -3813.7651     1060.884            0    757.21086    152307.36   -157939.22   -1043.4335    23867.228    231.99557    347.17994    1.1628589 
    1160    62.010573   -2805.5456    1027.0164   -3832.5621    1057.9262            0    777.84714    152269.56   -157937.89   -729.25379    23659.194    229.84839    343.97766    1.1301417 
    1180    62.973114   -2832.7144    1030.8608   -3863.5752    1084.2376            0    767.80175    152221.94   -157937.56   -1365.8515    23446.354    230.70875    345.24169    1.1814637 
    1200    63.943778   -2860.0062    1032.0824   -3892.0886    1078.2587            0    781.38106    152185.86   -157937.59   -1050.1069    23225.033    230.98216    345.65138    1.1817665 
    1220    64.923382   -2887.3006    1026.4756   -3913.7762    1073.1543            0    809.51178    152141.13   -157937.57    -956.1976    22997.996    229.72734    343.81693    1.0887098 
    1240    65.912183   -2912.0696    1020.0729   -3932.1425    1095.3889            0      826.297    152085.57    -157939.4   -534.84968    22767.897     228.2944    341.63565      1.15531 
    1260    66.908861   -2938.0025    1009.7902   -3947.7927    1120.1948            0    846.76965    152025.28   -157940.04   -581.84084    22538.229    225.99312    338.22714    1.0731061 
    1280    67.970707   -2960.3724    1046.6347   -4007.0071    1144.3297            0    866.43256    151921.62   -157939.39   -368.35961    22310.088      234.239    350.59018    1.0681573 
    1300    68.984941   -2983.8905    1039.0599   -4022.9504    1162.4788            0    878.40157    151876.66   -157940.49    -408.4644    22085.613    232.54373    348.07145    1.0232144 
    1320    70.043952   -3009.5808     969.8918   -3979.4726    1186.5907            0    935.08613    151836.22   -157937.36     431.8242    21865.457    217.06378    324.88371   0.98977725 
    1340    71.117119   -3028.1057    1016.1027   -4044.2084    1215.7197            0    933.65661    151744.63   -157938.22   -118.90908    21653.612    227.40587    340.39676   0.96927182 
    1360     72.19871   -3048.8293    986.21586   -4035.0452    1231.0917            0    974.10814    151697.47   -157937.72     485.3122    21448.458    220.71713    330.39668   0.91660237 
    1380    73.289545   -3067.6975    1046.3647   -4114.0622     1252.358            0    948.20869    151626.66   -157941.29   -131.77945    21251.912    234.17856    350.55699   0.95332826 
    1400    74.389534   -3091.6437     1003.804   -4095.4478    1223.2343            0    914.21639    151708.69   -157941.59   -228.59592    21060.319     224.6534    336.27611   0.95868112 
    1420    75.496459   -3117.9845    1017.2871   -4135.2716    1252.8701            0    934.95412    151617.13   -157940.22   -328.62774    20872.161    227.67095    340.80959   0.93833238 
    1440    76.611495   -3137.2342    990.73612   -4127.9703    1224.5861            0    925.81135    151661.05   -157939.42   -23.294916    20687.614    221.72878    331.93708   0.86871384 
    1460     77.73649   -3159.4947     1040.535   -4200.0297     1218.936            0    881.92261    151636.87   -157937.75   -581.29505    20507.346    232.87387    348.59778   0.96029886 
    1480    78.872562   -3183.8273    1037.9432   -4221.7705    1246.5207            0    908.21966    151561.59    -157938.1   -884.42345     20328.04    232.29381     347.7323   0.95226246 
    1500    80.110645   -3206.5826    1008.5663   -4215.1489    1236.8936            0    929.15034    151558.28   -157939.47   -91.502556    20149.349     225.7192    337.88949   0.92718943 
    1520    81.168804   -3228.1152     994.3422   -4222.4574    1276.2214            0    948.25706    151492.45   -157939.39   -262.49453    19974.554    222.53583    333.16141   0.83959152 
    1540    82.328931   -3248.9878    997.70762   -4246.6954    1273.2453            0    944.04689    151475.31    -157939.3   -310.12487    19802.717    223.28901    334.28865   0.84316615 
    1560    83.500822   -3268.9264    1001.6639   -4270.5903    1283.2174            0    972.25539    151413.47   -157939.53   -368.92162    19633.499    224.17444    335.57814   0.91870789 
    1580    84.681217   -3289.8506    972.05937   -4261.9099     1290.892            0    995.40503    151394.08   -157942.29     309.3174    19467.313    217.54888    325.64947   0.91261747 
    1600    85.872982   -3306.0485     999.0593   -4305.1078    1336.2852            0    1018.2817    151281.27   -157940.94    78.176324    19307.332    223.59152    334.68976   0.94786237 
    1620    87.166941    -3323.911    1023.7518   -4347.6628    1346.5659            0    1012.0297    151235.76   -157942.02    401.58054    19152.885    229.11774    342.98696   0.92107142 
    1640    88.373719   -3346.3201    1013.0953   -4359.4153    1368.3551            0    1038.3633    151174.74   -157940.87    115.49888    19004.339     226.7328    339.39185   0.96123977 
    1660    89.588199   -3366.6764    980.18808   -4346.8645    1385.5623            0    1066.3348    151143.21   -157941.97    785.51107    18860.969     219.3681    328.38652   0.89253119 
    1680    90.812635   -3382.4343    999.75094   -4382.1852    1367.9173            0    1045.8848    151142.33   -157938.32    549.73441    18726.008    223.74631      334.953   0.88544944 
    1700    92.044767   -3400.8462    996.00209   -4396.8483    1351.6629            0    1019.0394    151174.27   -157941.83    32.327852     18598.28    222.90731    333.67893   0.91827006 
    1720    93.284649   -3418.3313    989.38116   -4407.7125    1347.9882            0    1026.3475    151161.41   -157943.46    700.69172    18474.978    221.42553    331.45637   0.92100955 
    1740    94.538928   -3435.1347    964.16624    -4399.301    1357.6456            0    1051.1466    151135.74   -157943.84    477.68306      18358.2    215.78238      322.997   0.92157841 
    1760     95.90276   -3452.4681    996.08241   -4448.5506    1365.9896            0    1001.3994    151128.36    -157944.3   -77.655143    18246.618    222.92529    333.72093   0.88815023 
    1780    97.200704   -3470.0186    947.16368   -4417.1823    1357.1769            0    1006.9477    151162.27   -157943.57    100.19368      18137.3    211.97718     317.3159   0.87577473 
    1800    98.461648   -3484.6818    988.75293   -4473.4348    1367.5971            0     995.1924    151106.14   -157942.36   -208.37477    18030.204    221.28494    331.23294   0.94635825 
    1820    99.729642   -3503.5324     959.4974   -4463.0298    1386.9033            0    1035.1867    151057.26   -157942.38    196.09637    17924.392    214.73749    321.44422   0.89454363 
    1840    101.00392   -3518.4137    985.10207   -4503.5157     1425.227            0    1062.1927    150951.14   -157942.08    189.40933    17821.795    220.46787    330.02248   0.91769756 
    1860    102.28783   -3531.6076    978.71334   -4510.3209    1447.6145            0    1081.8026     150905.2   -157944.94    369.13672    17723.495    219.03805    327.84302   0.99005655 
    1880    103.57975   -3546.6803    982.10151   -4528.7818    1416.6032            0    1040.8725    150959.42   -157945.68    206.83653    17629.384    219.79633    328.97668    0.9960403 
    1900    104.81168   -3563.7438    961.75306   -4525.4969    1426.2883            0    1055.2567    150936.42   -157943.46    223.06115    17537.856    215.24231    322.15829   0.97986655 
    1920    106.04042   -3579.7815     953.8957   -4533.6772     1420.242            0    1053.3469    150938.67   -157945.93    264.48404    17448.909    213.48382    319.52979   0.96489929 
    1940    107.27692   -3592.4628    995.11883   -4587.5816    1434.5738            0    1036.2736    150885.59   -157944.02   -203.71783    17362.885    222.70964    333.32982    1.0238542 
    1960    108.52049   -3607.1225     959.8186   -4566.9411     1454.811            0    1091.6157    150830.59   -157943.96    412.09226    17278.194    214.80937    321.46995    1.0586113 
    1980    109.76987   -3621.5836    950.82575   -4572.4094    1481.3655            0    1148.5036     150742.3   -157944.58    1156.6083    17197.362    212.79675    318.42806    1.1085537 
    2000    111.02457   -3632.4321    939.77229   -4572.2044    1484.3457            0    1154.0077    150733.65   -157944.21    1008.3019    17124.028    210.32297     314.7467    1.0548599 
Loop time of 111.025 on 1 procs for 2000 steps with 2500 atoms

Pair  time (%) = 87.5509 (78.8572)
Bond  time (%) = 0.0493031 (0.0444073)
Kspce time (%) = 3.35179 (3.01896)
Neigh time (%) = 9.36055 (8.43106)
Comm  time (%) = 0.69479 (0.625798)
Outpt time (%) = 0.0108259 (0.00975088)
Other time (%) = 10.0064 (9.01281)

Nlocal:    2500 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    20348 ave 20348 max 20348 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    2.09326e+06 ave 2.09326e+06 max 2.09326e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2093261
Ave neighs/atom = 837.304
Ave special neighs/atom = 4
Neighbor list builds = 120
Dangerous builds = 16

